The SalzbergWordString kernel implements the Salzberg kernel.
It is described in
Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites A. Zien, G.Raetsch, S. Mika, B. Schoelkopf, T. Lengauer, K.-R. Mueller
Definition at line 29 of file SalzbergWordStringKernel.h.
default constructor
Definition at line 21 of file SalzbergWordStringKernel.cpp.
CSalzbergWordStringKernel | ( | int32_t | size, | |
CPluginEstimate * | pie, | |||
CLabels * | labels = NULL | |||
) |
constructor
size | cache size | |
pie | the plugin estimate | |
labels | optional labels to set prior from |
Definition at line 27 of file SalzbergWordStringKernel.cpp.
CSalzbergWordStringKernel | ( | CStringFeatures< uint16_t > * | l, | |
CStringFeatures< uint16_t > * | r, | |||
CPluginEstimate * | pie, | |||
CLabels * | labels = NULL | |||
) |
constructor
l | features of left-hand side | |
r | features of right-hand side | |
pie | the plugin estimate | |
labels | optional labels to set prior from |
Definition at line 37 of file SalzbergWordStringKernel.cpp.
~CSalzbergWordStringKernel | ( | ) | [virtual] |
Definition at line 51 of file SalzbergWordStringKernel.cpp.
void cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 292 of file SalzbergWordStringKernel.cpp.
float64_t compute | ( | int32_t | idx_a, | |
int32_t | idx_b | |||
) | [protected, virtual] |
compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object
idx_a | index a | |
idx_b | index b |
Implements CKernel.
Definition at line 317 of file SalzbergWordStringKernel.cpp.
int32_t compute_index | ( | int32_t | position, | |
uint16_t | symbol | |||
) | [protected] |
compute index of given symbol at given position
position | position | |
symbol | symbol |
Definition at line 116 of file SalzbergWordStringKernel.h.
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CStringKernel< uint16_t >.
Definition at line 90 of file SalzbergWordStringKernel.h.
virtual const char* get_name | ( | void | ) | const [virtual] |
return the kernel's name
Reimplemented from CStringKernel< uint16_t >.
Definition at line 96 of file SalzbergWordStringKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< uint16_t >.
Definition at line 56 of file SalzbergWordStringKernel.cpp.
set prior probs
pos_prior_ | positive prior | |
neg_prior_ | negative prior |
Definition at line 61 of file SalzbergWordStringKernel.h.
void set_prior_probs_from_labels | ( | CLabels * | labels | ) |
set prior probs from labels
labels | labels to set prior probabilites from |
Definition at line 352 of file SalzbergWordStringKernel.cpp.
CPluginEstimate* estimate [protected] |
the plugin estimate
Definition at line 125 of file SalzbergWordStringKernel.h.
bool initialized [protected] |
if kernel is initialized
Definition at line 153 of file SalzbergWordStringKernel.h.
float64_t* ld_mean_lhs [protected] |
ld mean left-hand side
Definition at line 138 of file SalzbergWordStringKernel.h.
float64_t* ld_mean_rhs [protected] |
ld mean right-hand side
Definition at line 140 of file SalzbergWordStringKernel.h.
mean
Definition at line 128 of file SalzbergWordStringKernel.h.
negative prior
Definition at line 151 of file SalzbergWordStringKernel.h.
int32_t num_params [protected] |
number of params
Definition at line 143 of file SalzbergWordStringKernel.h.
int32_t num_symbols [protected] |
number of symbols
Definition at line 145 of file SalzbergWordStringKernel.h.
positive prior
Definition at line 149 of file SalzbergWordStringKernel.h.
float64_t* sqrtdiag_lhs [protected] |
sqrt diagonal of left-hand side
Definition at line 133 of file SalzbergWordStringKernel.h.
float64_t* sqrtdiag_rhs [protected] |
sqrt diagonal of right-hand side
Definition at line 135 of file SalzbergWordStringKernel.h.
sum m2 s2
Definition at line 147 of file SalzbergWordStringKernel.h.
variance
Definition at line 130 of file SalzbergWordStringKernel.h.